[ome-users] [Bio-Formats] JPEG-XR via CZI

[Douglas Richardson]

Yes, you can turn off the compression. You still get a .czi container, but
the data is no longer compressed by JPEG XR.  Depending on how large the
total area you need to scan is, and how many colors you have (if doing
fluorescence), the file size can become so large that it's easier to save
as JPEG XR.  Either way, I believe you still have to split the file (if
it's large) and fuse each region into a single tile before Bioformats can
properly display it.

-Doug



On Fri, Jul 31, 2015 at 10:53 AM, Damir Sudar <dsudar at lbl.gov> wrote:

> Hi Doug and all,
> As an alternative to exporting/converting to tiff/bigtiff, is it an option
> to turn off the JpegXR compression during acquisition and then use the
> resulting czi files to import into OMERO or read with BioFormats?
> Thanks,
> - Damir
>
> On Fri, Jul 31, 2015 at 5:23 AM, Doug Richardson <ds.richardson at gmail.com>
> wrote:
>
>> Hi Alexandre,
>>
>> If you update to ZEN2 it has much improved support for tif or bigtif
>> export (both recognized by Fiji/Bioformats). Although it takes a very long
>> time to open the largest files. During export we subset by scene and
>> channel and this makes things manageable.
>>
>> If you don't have ZEN2 you can get the somewhat clunkier stand alone czi
>> to tif converter. Linked from here on our website:
>> http://hcbi.fas.harvard.edu/resources_software
>>
>> Zeiss should also be able to help you with this.
>>
>> Doug
>>
>>
>>
>> Sent from my iPhone
>>
>> On Jul 31, 2015, at 8:08 AM, Alexandre Dufour <adufour at pasteur.fr> wrote:
>>
>> Thanks for the prompt reply Josh.
>>
>> Just for my information: since it appears this isn’t going to be done
>> anytime soon, and we do have a lot of users no this new machine, what
>> alternative solution should I lean towards (in other words, what should I
>> tell them)?
>>
>> Cheers
>> Alexandre
>>
>>
>> On 31 Jul 2015, at 14:06, Josh Moore <josh at glencoesoftware.com> wrote:
>>
>> On Fri, Jul 31, 2015 at 1:44 PM, Alexandre Dufour <adufour at pasteur.fr>
>> wrote:
>>
>> Hi everyone,
>>
>>
>> Hi Alexandre,
>>
>>
>> I was trying to fiddle with a CZI file that has JPEG-XR compression, alas
>> it
>> won’t open via the latest Bio-Formats (official or nightly), with the
>> following error:
>>
>> loci.formats.UnsupportedCompressionException: JPEG-XR not yet supported
>>
>> After digging through some archives, I found:
>> - this ticket: https://trac.openmicroscopy.org/ome/ticket/8493
>> - this PR: https://github.com/openmicroscopy/bioformats/pull/1014
>> which suggests that the issue had been fixed over a year ago, hence my
>> surprise.
>>
>>
>> Sorry for the surprise. We did indeed start the work on a JPEG-XR
>> codec but realized that we weren't going to be able to complete it and
>> achieve our other goals. The PR you reference (8493) added as the
>> title says the "initial structure" for the package, but the critical
>> methods are not yet implemented. Similarly, all the JPEG-XR tickets
>> (8493 and the 12 associated tasks) were all closed: "needsfunding"
>> about 3 months ago:
>>
>>  Resolution set to needfunding
>>  Status changed from accepted to closed
>>
>> We're certainly also interested in seeing this supported, but at the
>> moment, no work is ongoing.
>>
>> All the best,
>> ~Josh
>>
>>
>>
>> I have such a sample with me if you are interested (FTP access preferred).
>>
>> Cheers
>> Alexandre
>>
>> —
>> Alexandre Dufour, PhD
>>
>> Senior Research Fellow @ Biological Image Analysis group
>> Institut Pasteur, Dpt. of Cell Biology & Infection, Paris campus (France)
>> CNRS UMR 3691 “Pathological and Physiological Cell Dynamics”
>>
>> Meet Icy, the next-generation Bioimage Informatics platform
>>
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>
>
> --
> Damir Sudar - Staff Scientist
> Lawrence Berkeley Laboratory / Life Sciences Division
> One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
> T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov
>
> Visiting Scientist, Oregon Health and Science University
>
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